In addition to the stipulations listed below, I have also noticed that apbs can't handle a pdb file that has coordinate columns that touch each other such as this example:

                                      this column
ATOM     78  N   GLY A  38      66.914  66.219-103.497  1.00 18.01      A  
ATOM     79  CA  GLY A  38      66.309  66.763-104.698  1.00 20.04      A  
ATOM     80  C   GLY A  38      65.598  68.007-104.199  1.00 20.96      A  
ATOM     81  O   GLY A  38      64.432  68.267-104.508  1.00 23.61      A  

I've needed to transform the coordinates of my molecule so that this kind of thing doesn't happen.
(realspace_transform.inp in CNS works.)

Hope this helps.


You have to see if you are getting the .dx file. The default of  the program is to put it at the same directory where it was installed, along with the other temporary files: .in, .pqr and .pdb. In case of not, I got the same problem and the solution was: the PDB that you load can`t have chain ID, the aminoacids can`t have alternate conformations and the program only accepts the standard residues. If everything is all right with your PBD, after run the APBS you gotta have the .dx at this directory. Once you got the .dx (the pymol will show the click at the update (on Visualization) and then show.
Hope this help!

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